DebiChem Molecular mechanics packages

Adun es un simulador biomolecular que además posee capacidades de gestión y análisis de datos. Ha sido desarrollado por el Laboratorio de Biofísica y Bioquímica Computacional, que forma parte de la Unidad de Investigación de Informática Biomédica de la Universidad Pompeu Fabra.

Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

• Molecular modeller with automatic force-field based geometry optimization
• Molecular Mechanics including constraints and conformer searches
• Visualization of molecular orbitals and general isosurfaces
• Visualization of vibrations and plotting of vibrational spectra
• Support for crystallographic unit cells
• Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
• Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.

GROMACS es un paquete versátil para representar dinámica molecular. Esto es, simular las ecuaciones Newtonianas de movimiento para sistemas con cientos o incluso millones de partículas.

Está diseñado principalmente para moléculas bioquímicas como proteínas o lípidos que tienen un montón de complicadas interacciones relacionadas. Pero dado que GROMACS es extremadamente rápido calculando las interacciones no relacionadas (que normalmente dominan las simulaciones) muchos grupos también lo usan en investigaciones de sistemas no biológicos como polímeros por ejemplo.

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors.

csg is Votca's coarse-graining engine.

VMD stands for Visual Molecular Dynamics. While text books and even structure databases because of technical problems only present static pictures of proteins or DNA, for the understanding of the properties of those molecules their vibration or their movement in general is important.

The movements itself are calculated by molecular dynamics programs, such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The latter two are already in the distribution, we have package build instructions for Rosetta.

VMD has a series of nice features, from displaying through animation to analysing. It can be scripted, clustered, and runs on all common OS. Its license does not allow to redistribute a Debian package. But to share these build instructions for such a package is just fine.